1qb4

CRYSTAL STRUCTURE OF MN(2+)-BOUND PHOSPHOENOLPYRUVATE CARBOXYLASE

Method: X-RAY DIFFRACTION D_max: 89.0 Å Quality: EXCELLENT

SAXS 散射曲线 SAXS Profile

P(r) 距离分布 P(r) Distribution

下载 Download SAXS (.dat) P(r) (.pr.out) CIF

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	1qb4
沉积日期 deposition_date	1999-04-30
结构标题 title	CRYSTAL STRUCTURE OF MN(2+)-BOUND PHOSPHOENOLPYRUVATE CARBOXYLASE
关键词 keywords	ALPHA BETA BARREL, LYASE; LYASE
实验方法 method	X-RAY DIFFRACTION

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2. SAXS 参数 (CRYSOL 理论计算) 2. SAXS Parameters (CRYSOL)

回转半径 Rg (Guinier) rg_guinier	29.43 Å
回转半径 Rg (电子) rg_electron	28.30 Å
零角强度 I(0) i0	150183000.00
分子量 molecular_weight	97327.0 kDa
排除体积 excluded_volume	122070 Å³
包络体积 envelope_volume	147770 Å³
水化壳体积 shell_volume	42125 Å³
包络直径 envelope_diameter	95.1 Å
壳层 Rg shell_rg	36.89 Å
包络 Rg envelope_rg	28.43 Å
形状 Rg shape_rg	28.31 Å
总 Rg total_rg	29.06 Å
总原子数 total_atoms	6845
残基数 n_residues	874
球谐函数阶数 n_harmonics	20
q 范围 q_range	— – 0.5000 Å⁻¹
数据点数 n_points	101
壳层类型 shell_type	directional
溶剂电子密度 solvent_density	0.3340 e/Å³
壳层衬度 contrast_shell	0.0300 e/Å³
CRYSOL 版本 crysol_version	4.1.3

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3. P(r) 距离分布 (GNOM 反演) 3. P(r) Analysis (GNOM)

最大尺寸 Dmax dmax	89.0 Å
Rg (实空间) rg_real	29.27 Å
Rg 误差 (实空间) rg_real_error	0.59 Å
I(0) (实空间) i0_real	1.5020e+08
I(0) 误差 (实空间) i0_real_error	2.1130e+06
Rg (倒空间) rg_reciprocal	29.34 Å
I(0) (倒空间) i0_reciprocal	150200000.0000
解质量估计 total_estimate	0.9033
解质量评级 solution_quality	EXCELLENT a EXCELLENT solution
P(r) 峰数 n_peaks	2
主峰位置 r_peak_primary	37.9 Å
偏度 Skewness skewness	0.151
峰度 Kurtosis kurtosis	-0.465
角度范围 angular_range	— – 0.2700 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	51070000.0000
实空间数据点数 n_real_points	55
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.944; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.981; Smooth: 0.927

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4. 晶体学与实验 4. Crystallography & Experiment

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5. 实体与聚合体信息 (4)

Entity 1 polymer

描述 description	PHOSPHOENOLPYRUVATE CARBOXYLASE
分子量 formula_weight	99175.5 kDa
EC 编号 ec_number	4.1.1.31
来源方法 src_method	man
拷贝数 entity_count	1

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A
原子数 atom_count	6926

MNEQYSALRSNVSMLGKVLGETIKDALGEHILERVETIRKLSKSSRAGNDANRQELLTTLQNLSNDELLPVARAFSQFLNLANTAEQYHSISPKGEAASNPEVIARTLRKLKNQPELSEDTIKKAVESLSLELVLTAHPTEITRRTLIHKMVEVNACLKQLDNKDIADYEHNQLMRRLRQLIAQSWHTDEIRKLRPSPVDEAKWGFAVVENSLWQGVPNYLRELNEQLEENLGYKLPVEFVPVRFTSWMGGDRDGNPNVTADITRHVLLLSRWKATDLFLKDIQVLVSELSMVEATPELLALVGEEGAAEPYRYLMKNLRSRLMATQAWLEARLKGEELPKPEGLLTQNEELWEPLYACYQSLQACGMGIIANGDLLDTLRRVKCFGVPLVRIDIRQESTRHTEALGELTRYLGIGDYESWSEADKQAFLIRELNSKRPLLPRNWQPSAETREVLDTCQVIAEAPQGSIAAYVISMAKTPSDVLAVHLLLKEAGIGFAMPVAPLFETLDDLNNANDVMTQLLNIDWYRGLIQGKQMVMIGYSDSAKDAGVMAASWAQYQAQDALIKTCEKAGIELTLFHGRGGSIGRGGAPAHAALLSQPPGSLKGGLRVTEQGEMIRFKYGLPEITVSSLSLYTGAILEANLLPPPEPKESWRRIMDELSVISCDVYRGYVRENKDFVPYFRSATPEQELGKLPLGSRPAKRRPTGGVESLRAIPWIFAWTQNRLMLPAWLGAGTALQKVVEDGKQSELEAMCRDWPFFSTRLGMLEMVFAKADLWLAEYYDQRLVDKALWPLGKELRNLQEEDIKVVLAIANDSHLMADLPWIAESIQLRNIYTDPLNVLQAELLHRSRQAEKEGQEPDPRVEQALMVTIAGIAAGMRNTG

来源 Source

来源生物 organism	Escherichia coli
NCBI 分类编号 ncbi_taxonomy_id	562
宿主生物 host_organism	Escherichia coli

Entity 2 non-polymer

描述 description	MANGANESE (II) ION
分子量 formula_weight	54.9 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

Entity 3 non-polymer

描述 description	ASPARTIC ACID
分子量 formula_weight	133.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

Entity 4 water

描述 description	water
分子量 formula_weight	18.0 kDa
来源方法 src_method	nat
拷贝数 entity_count	81

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6. 折叠分类 (SCOP + CATH) 1 domains

SCOP 2.08 (1 domains)

结构域编号 domain_id	d1qb4a_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.1 — TIM beta/alpha-barrel
超家族 Superfamily superfamily	c.1.12 — Phosphoenolpyruvate/pyruvate domain
家族 Family family	c.1.12.3 — Phosphoenolpyruvate carboxylase

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7. 引用文献 (2)

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晶胞边长 a length_a	117.750 Å
晶胞边长 b length_b	248.410 Å
晶胞边长 c length_c	83.470 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	90.00 °
晶胞夹角 γ angle_gamma	90.00 °
晶胞分子数 Z z_pdb	8

空间群 space_group	I 2 2 2
空间群编号 int_tables_number	23
晶系 crystal_system	—

分辨率 resolution	2.600 Å
最低分辨率 resolution_low	20.000 Å
R 因子 r_factor	0.2210
R_work r_work	0.2230
R_free r_free	0.2610

fit	/app/data/saxs_computation/qb/1qb4/1qb4.fit
pddf	/app/data/pr_computation/qb/1qb4/1qb4.pr.out
profile	/app/data/saxs_computation/qb/1qb4/1qb4.dat